Partnership for a cross-disciplinary approach to the ecology of antimicrobial drug resistance in Kenya

Lead Research Organisation: University of Liverpool
Department Name: Institute of Infection and Global Health


Antibacterial resistance (ABR) is a significant threat to the future of effective healthcare and veterinary care. Globally, we are dependent on antibiotics for treating common as well as severe infections, but we abuse the value of these compounds by using them irrationally. In Kenya, as in many other countries, antibiotics are prescribed un-necessarily and without properly identifying the micro-organims being targeted, a fact that often leads to treatment failures. In agriculture, antibiotics are often used directly by farmers, as they are readily available on the market without prescription. Kenya is a country undergoing a demographic transition towards urbanisation, with over half the population expected to be in urban zones by the middle of this century. Many of these people are likely to live in low income settlements (eg 60% of residents of Nairobi, the capital, live in low income settlements = slums). Provision of high quality heath care is lacking in such sites. Further, with more people living in towns and cities, the pressure will be on farmers to produce more food more efficiently, and a key part of this - as has been the case in more developed economies - will be to use antibiotic drugs. These factors combine to produce a great deal of risk for highly drug resistant micro-organisms to emerge. Essential in preventing this will be to collect high quality data in hospitals and on farms, to understand what levels of resistance are present now, and how the organisms share their genes, a process that can result in rapid spread of resistant traits. A key aspects of this is also to understand how antibacterial drugs are used in practice, how they are procured and what drives individual and collective decision making about their use. Our programme will investigate these different aspects and work with partners in Kenya and internationally who make policy, in order to develop long term surveillance tools, plans to limit the spread of resistance and advice to the public to conserve these important drugs.

Technical Summary

In Kenya and elsewhere, the antibiotic landscape for healthcare and livestock production is shaped by poor regulation and irrational drug use. There is a need for related evidence-based policy and the implementation plans for such policy. We will conduct in depth research in clinical and community settings to understand patterns of resistance, transmission of bacteria and their resistance determinants and genome based studies of resistance evolution. This will be combined with social and economic approaches to quantify the burden of antibacterial infection, the behavioural aspects of drug prescribing and use and the risks of mixing of bacterial populations between clinical settings, the community and the food systems that link them. Our approach is to build a strong network of antibacterial surveillance to monitor microbial ecology, and identify hotspots of selective pressure.
Our objectives are:
1) Surveillance in health care settings. We will establish longitudinal and cross sectional surveillance in clinical settings and explore changes in the diversity of bacterial flora with differing care pathways and drug exposure.
2) Community based longitudinal monitoring of ABR in livestock producers. We will recruit commercial farmers in to a series of longitudinal cohorts and monitor their bacterial ecology over time.
3) Microbiological dynamics within the household. We will explore the longitudinal dynamics of bacterial populations in humans, their animals and the immediate farm environment, as well as the products leaving the farms for market.
4) Microbiology and sequencing. We will develop robust microbiological and sequence-based approaches to quantifying bacterial diversity and drug sensitivity
5) Human behaviour and decision-making. We will emphasise the study of the social and economic environment in which antibiotic use takes place, both in domestic animals and humans and develop policy frameworks to limit irrational use.

Planned Impact

In our Pathways to Impact document we have outlined partnerships we have enrolled with the ABR policy community in Kenya. Reviewing the recently published National Action Plan on Prevention and Containment of Antimicrobial Resistance, 2017-2022 (Government of Kenya, May 2017), developed in partnership with the Fleming Fund, it is clear that our proposed scientific research is in demand. Quoted below, the Plan's aims include:
- Increasing knowledge and understanding of antimicrobial resistance and antimicrobial use, especially in the healthcare, food, and livestock production sectors;
- Understanding the state of AMR emergence and prevalence, and use of antimicrobials (including surveillance and monitoring), and to assess the risk of emergence;
- Enhancing proper infection prevention and control;
- Ensuring antimicrobial stewardship (AMS) in order to reduce antimicrobial-resistant organisms;
- Accelerating research on the mechanism of AMR emergence and transmission, and its impact on social economy.
Our scientific outputs will be in demand by this policy community to take action in Kenya within the lifespan of the Consortium award, and our programme will be geared towards providing the best quality evidence available.

We will also have impact in training a cohort of future leaders in this field. All the co-Is are committed to training and capacity building, and all manage undergraduate, Masters and PhD level students with diverse funding sources. Aside from registered students, in Kenya, Fèvre's team manages annual cohorts of Kenya Field Epidemiology and Laboratory Training (FELTP) residents, young medical and veterinary clinicians who will benefit from our Consortium phase through specific training on the epidemiology and management of ABR. Already in the Development phase award we will engage 3 such individuals. Birungi, through the BecA Africa Bioscience Challenge Fund (ABCF) hosts emerging scientists from a range of national research institutions, providing mentorship, skills and access to top class facilities. Revathi hosts trainee microbiologists at Aga Khan; our Consortium phase would provide specific training in diagnosis and management of ABR for such trainees. Bukachi is currently engaged with UK-Kenya training in social anthropology. Kariuki is deeply engaged in training cohorts of young Kenyan microbiologists and laboratory technicians. Our activities in Kenya will also provide a template for trainees from across the Horn of Africa funded by our recent RCUK Capability and Capacity Strengthening Award (involving Universities of Liverpool, Nairobi, KEMRI and BecA). The programme will also enhance partnerships between the Kenya-based institutions, providing opportunities for further collaborative activity.


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Description Key information about AMR in an East African context that has led to the design of the National Action Plan in Kenya, with Fleming Fund funding and co-implemented by our team
Exploitation Route Design of the National Action Plan for AMR
Sectors Agriculture, Food and Drink,Environment,Healthcare

Description Public education on AMR through a training video endorsed by the Government of Kenya, and available here Establishment of the National Action Plan on AMR, which our team are responsible for implementing in the agriculture sector in Kenya
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Healthcare
Impact Types Societal,Policy & public services

Description Natioanl AMR Value Chain Survey
Geographic Reach Africa 
Policy Influence Type Gave evidence to a government review
Impact Conducted a national agricultural value chain survey for antimicrobial drugs in Kenya
Description CGIAR AMR Hub
Amount $500,000 (USD)
Funding ID A4NH CGIAR AMR Hub 
Organisation International Livestock Research Institute (ILRI) 
Sector Charity/Non Profit
Country Kenya
Start 02/2019 
End 02/2022
Description Fleming Fund Kenya Country Grant
Amount £6,000,000 (GBP)
Funding ID MML.574394-01681708-SUB 
Organisation Fleming Fund 
Sector Charity/Non Profit
Start 08/2019 
End 04/2021
Description A4NH 
Organisation International Food Policy Research Institute (IFPRI)
Department Agriculture for Nutrition and Health
Country United States 
Sector Charity/Non Profit 
PI Contribution Technical expertise
Collaborator Contribution Funding for sub-projects (eg on human nutrition in urban value chains), as well as technical staff support and some consumables
Impact Interdiciplinary. Outputs still in preparation
Start Year 2013
Description Aga Khan 
Organisation Aga Khan Hospital
Country Kenya 
Sector Hospitals 
PI Contribution Sharing of expertise and samples
Collaborator Contribution Sharing of expertise and samples
Impact Materials shared for whole genome sequencing
Start Year 2018
Description DVS 
Organisation Veterinary Services Department
Country Kenya 
Sector Learned Society 
PI Contribution Training for fresh veterinary graduates who are attached to our programme at no cost to us for 52 weeks
Collaborator Contribution Partners are administering contracts for newly qualified vets who are attached to our programme
Impact Wide ranging contributions to project outputs more generally
Start Year 2018
Description Farmers Choice 
Organisation Farmer's Choice Ltd
Country United Kingdom 
Sector Private 
PI Contribution Provision of data and the design of a data capture system for the farms
Collaborator Contribution Close collaborative relationship in understanding the pig industry in Kenya; provision of manpower and access to on farm resources.
Impact A handheld data collection system developed by a commercial partner
Start Year 2018
Description Kenya FELTP 
Organisation Jomo Kenyatta University of Agriculture and Technology (JKUAT)
Department Kenya Field Epidemiology and Laboratory Training Program
Country Kenya 
Sector Academic/University 
PI Contribution We train FELTP residents in our programme
Collaborator Contribution Provide 3x full time trainees every year (total of 6 trainees at any given time) at no cost to our programme. Effectively, we are given 6 free members of full time staff.
Impact MSc theses x3 so far Papers x 3 in preparation 6x theses expected over the next 2 years
Start Year 2015
Description Kenya VMD 
Organisation Government of Kenya
Country Kenya 
Sector Public 
PI Contribution We have partnered with the Kenya VMD to undertake a value chain analysis of antimicrobial drugs in Kenya. We provided an intern to undertake data entry, and we provided draft questionnaires and technical input to survey design. We will jointly write a paper.
Collaborator Contribution Partner has provided data collected through government funded work.
Impact No yet
Start Year 2017
Description ZDU Kenya 
Organisation Government of Kenya
Department Zoonotic Disease Unit
Country Kenya 
Sector Public 
PI Contribution ZDU is a policy partner to whom we have contributed policy advice for national level policy making
Collaborator Contribution Facilitation to work in Kenya
Impact Formal advice to policy fora. Involvment of the PI in two national task forces.
Start Year 2012
Description World Antibiotic Awareness Week 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Kenya Government and FAO Regional World Antibiotic Awareness Week Information event, Theme: Tackling AMR Together; 21-22 November 2019
Year(s) Of Engagement Activity 2019